Commit 943216c5 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1732 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent b729a796

src/COLLOID/pair_lubricate.cpp

+6 −4
Original line number Diff line number Diff line
@@ -86,6 +86,7 @@ void PairLubricate::compute(int eflag, int vflag) 
  int nlocal = atom->nlocal;

  int newton_pair = force->newton_pair;

  int omega_flag = atom->omega_flag;

  double vxmu2f = force->vxmu2f;



  inum = list->inum;

  ilist = list->ilist;
@@ -198,16 +199,17 @@ void PairLubricate::compute(int eflag, int vflag) 
        h_sep = r - 2.0*radi;



	if (flag1)

	  a_squeeze = (3.0*PI*mu*2.0*radi/2.0) * (2.0*radi/4.0/h_sep); 

	  a_squeeze = vxmu2f * 

	    (3.0*PI*mu*2.0*radi/2.0) * (2.0*radi/4.0/h_sep); 

	if (flag2) 

	  a_shear = (PI*mu*2.*radi/2.0) *

	  a_shear = vxmu2f * (PI*mu*2.*radi/2.0) *

	    log(2.0*radi/2.0/h_sep)*(2.0*radi+h_sep)*(2.0*radi+h_sep)/4.0;

	if (flag3) 

	  a_pump = (PI*mu*pow(2.0*radi,4)/8.0) *

	  a_pump = vxmu2f * (PI*mu*pow(2.0*radi,4)/8.0) *

	    ((3.0/20.0) * log(2.0*radi/2.0/h_sep) + 

	     (63.0/250.0) * (h_sep/2.0/radi) * log(2.0*radi/2.0/h_sep));

	if (flag4)

	  a_twist = (PI*mu*pow(2.0*radi,4)/4.0) *

	  a_twist = vxmu2f * (PI*mu*pow(2.0*radi,4)/4.0) *

	    (h_sep/2.0/radi) * log(2.0/(2.0*h_sep));



        if (h_sep >= cut_inner[itype][jtype]) {

src/fix_nph.cpp

+17 −15
Original line number Diff line number Diff line
@@ -37,6 +37,8 @@ using namespace LAMMPS_NS; 
#define MIN(A,B) ((A) < (B)) ? (A) : (B)

#define MAX(A,B) ((A) > (B)) ? (A) : (B)



enum{XYZ,XY,YZ,XZ,ANISO};



/* ---------------------------------------------------------------------- */



FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
@@ -55,7 +57,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : 
  if (strcmp(arg[3],"xyz") == 0) {

    if (narg < 7) error->all("Illegal fix nph command");



    press_couple = 0;

    press_couple = XYZ;

    p_start[0] = p_start[1] = p_start[2] = atof(arg[4]);

    p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[5]);

    p_period[0] = p_period[1] = p_period[2] = atof(arg[6]);
@@ -66,16 +68,16 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : 
    }



  } else {

    if (strcmp(arg[3],"xy") == 0) press_couple = 1;

    else if (strcmp(arg[3],"yz") == 0) press_couple = 2;

    else if (strcmp(arg[3],"xz") == 0) press_couple = 3;

    else if (strcmp(arg[3],"aniso") == 0) press_couple = 4;

    if (strcmp(arg[3],"xy") == 0) press_couple = XY;

    else if (strcmp(arg[3],"yz") == 0) press_couple = YZ;

    else if (strcmp(arg[3],"xz") == 0) press_couple = XZ;

    else if (strcmp(arg[3],"aniso") == 0) press_couple = ANISO;

    else error->all("Illegal fix nph command");



    if (narg < 11) error->all("Illegal fix nph command");



    if (domain->dimension == 2 && 

	(press_couple == 1 || press_couple == 2 || press_couple == 3))

	(press_couple == XY || press_couple == YZ || press_couple == XZ))

      error->all("Invalid fix nph command for a 2d simulation");



    if (strcmp(arg[4],"NULL") == 0) {
@@ -117,7 +119,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : 
  allremap = 1;



  int iarg;

  if (press_couple == 0) iarg = 7;

  if (press_couple == XYZ) iarg = 7;

  else iarg = 11;



  while (iarg < narg) {
@@ -134,7 +136,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : 
    } else error->all("Illegal fix nph command");

  }



  // error checks

  // check for periodicity in controlled dimensions



  if (p_flag[0] && domain->xperiodic == 0)

    error->all("Cannot use fix nph on a non-periodic dimension");
@@ -313,7 +315,7 @@ void FixNPH::setup(int vflag) 
  p_target[1] = p_start[1];

  p_target[2] = p_start[2];



  if (press_couple == 0) {

  if (press_couple == XYZ) {

    double tmp = temperature->compute_scalar();

    tmp = pressure->compute_scalar();

  } else {
@@ -426,7 +428,7 @@ void FixNPH::final_integrate() 


  // compute new pressure



  if (press_couple == 0) {

  if (press_couple == XYZ) {

    double tmp = temperature->compute_scalar();

    tmp = pressure->compute_scalar();

  } else {
@@ -598,21 +600,21 @@ void FixNPH::couple() 
{

  double *tensor = pressure->vector;



  if (press_couple == 0)

  if (press_couple == XYZ)

    p_current[0] = p_current[1] = p_current[2] = pressure->scalar;

  else if (press_couple == 1) {

  else if (press_couple == XY) {

    double ave = 0.5 * (tensor[0] + tensor[1]);

    p_current[0] = p_current[1] = ave;

    p_current[2] = tensor[2];

  } else if (press_couple == 2) {

  } else if (press_couple == YZ) {

    double ave = 0.5 * (tensor[1] + tensor[2]);

    p_current[1] = p_current[2] = ave;

    p_current[0] = tensor[0];

  } else if (press_couple == 3) {

  } else if (press_couple == XZ) {

    double ave = 0.5 * (tensor[0] + tensor[2]);

    p_current[0] = p_current[2] = ave;

    p_current[1] = tensor[1];

  } if (press_couple == 4) {

  } else if (press_couple == ANISO) {

    p_current[0] = tensor[0];

    p_current[1] = tensor[1];

    p_current[2] = tensor[2];

src/fix_npt.cpp

+16 −15
Original line number Diff line number Diff line
@@ -37,6 +37,7 @@ using namespace LAMMPS_NS; 
#define MAX(A,B) ((A) > (B)) ? (A) : (B)



enum{NOBIAS,BIAS};

enum{XYZ,XY,YZ,XZ,ANISO};



/* ---------------------------------------------------------------------- */
@@ -63,7 +64,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : 
  if (strcmp(arg[6],"xyz") == 0) {

    if (narg < 10) error->all("Illegal fix npt command");



    press_couple = 0;

    press_couple = XYZ;

    p_start[0] = p_start[1] = p_start[2] = atof(arg[7]);

    p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[8]);

    p_period[0] = p_period[1] = p_period[2] = atof(arg[9]);
@@ -74,16 +75,16 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : 
    }



  } else {

    if (strcmp(arg[6],"xy") == 0) press_couple = 1;

    else if (strcmp(arg[6],"yz") == 0) press_couple = 2;

    else if (strcmp(arg[6],"xz") == 0) press_couple = 3;

    else if (strcmp(arg[6],"aniso") == 0) press_couple = 4;

    if (strcmp(arg[6],"xy") == 0) press_couple = XY;

    else if (strcmp(arg[6],"yz") == 0) press_couple = YZ;

    else if (strcmp(arg[6],"xz") == 0) press_couple = XZ;

    else if (strcmp(arg[6],"aniso") == 0) press_couple = ANISO;

    else error->all("Illegal fix npt command");



    if (narg < 14) error->all("Illegal fix npt command");



    if (domain->dimension == 2 && 

	(press_couple == 1 || press_couple == 2 || press_couple == 3))

	(press_couple == XY || press_couple == YZ || press_couple == XZ))

      error->all("Invalid fix npt command for a 2d simulation");



    if (strcmp(arg[7],"NULL") == 0) {
@@ -125,7 +126,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : 
  allremap = 1;



  int iarg;

  if (press_couple == 0) iarg = 10;

  if (press_couple == XYZ) iarg = 10;

  else iarg = 14;



  while (iarg < narg) {
@@ -142,7 +143,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : 
    } else error->all("Illegal fix npt command");

  }



  // error checks

  // check for periodicity in controlled dimensions



  if (p_flag[0] && domain->xperiodic == 0)

    error->all("Cannot use fix npt on a non-periodic dimension");
@@ -322,7 +323,7 @@ void FixNPT::setup(int vflag) 
  p_target[2] = p_start[2];



  t_current = temperature->compute_scalar();

  if (press_couple == 0) {

  if (press_couple == XYZ) {

    double tmp = pressure->compute_scalar();

  } else {

    temperature->compute_vector();
@@ -473,7 +474,7 @@ void FixNPT::final_integrate() 
  // compute new T,P



  t_current = temperature->compute_scalar();

  if (press_couple == 0) {

  if (press_couple == XYZ) {

    double tmp = pressure->compute_scalar();

  } else {

    temperature->compute_vector();
@@ -687,21 +688,21 @@ void FixNPT::couple() 
{

  double *tensor = pressure->vector;



  if (press_couple == 0)

  if (press_couple == XYZ)

    p_current[0] = p_current[1] = p_current[2] = pressure->scalar;

  else if (press_couple == 1) {

  else if (press_couple == XY) {

    double ave = 0.5 * (tensor[0] + tensor[1]);

    p_current[0] = p_current[1] = ave;

    p_current[2] = tensor[2];

  } else if (press_couple == 2) {

  } else if (press_couple == YZ) {

    double ave = 0.5 * (tensor[1] + tensor[2]);

    p_current[1] = p_current[2] = ave;

    p_current[0] = tensor[0];

  } else if (press_couple == 3) {

  } else if (press_couple == XZ) {

    double ave = 0.5 * (tensor[0] + tensor[2]);

    p_current[0] = p_current[2] = ave;

    p_current[1] = tensor[1];

  } if (press_couple == 4) {

  } else if (press_couple == ANISO) {

    p_current[0] = tensor[0];

    p_current[1] = tensor[1];

    p_current[2] = tensor[2];

src/force.h

+1 −0
Original line number Diff line number Diff line
@@ -26,6 +26,7 @@ class Force : protected Pointers { 
  double nktv2p;                     // conversion of NkT/V to pressure

  double qqr2e;                      // conversion of q^2/r to energy

  double qe2f;                       // conversion of qE to force

  double vxmu2f;                     // conversion of vx mu to force

  double dielectric;                 // dielectric constant

  double qqrd2e;                     // q^2/r to energy w/ dielectric constant

src/min_cg.cpp

+1 −0
Original line number Diff line number Diff line
@@ -186,6 +186,7 @@ void MinCG::run() 
    eng_force(&ntmp,&xtmp,&htmp,&etmp);

    output->write(update->ntimestep);

  }



  timer->barrier_stop(TIME_LOOP);



  // delete fix at end of run, so its atom arrays won't persist

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